<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
          "DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
  <title>Priithon.readerHIS</title>
  <link rel="stylesheet" href="epydoc.css" type="text/css" />
  <script type="text/javascript" src="epydoc.js"></script>
</head>

<body bgcolor="white" text="black" link="blue" vlink="#204080"
      alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="Priithon-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://code.google.com/p/priithon">Priithon</a></th>
          </tr></table></th>
  </tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
  <tr valign="top">
    <td width="100%">
      <span class="breadcrumbs">
        <a href="Priithon-module.html">Package&nbsp;Priithon</a> ::
        Module&nbsp;readerHIS
      </span>
    </td>
    <td>
      <table cellpadding="0" cellspacing="0">
        <!-- hide/show private -->
        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
        <tr><td align="right"><span class="options"
            >[<a href="frames.html" target="_top">frames</a
            >]&nbsp;|&nbsp;<a href="Priithon.readerHIS-module.html"
            target="_top">no&nbsp;frames</a>]</span></td></tr>
      </table>
    </td>
  </tr>
</table>
<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module readerHIS</h1><p class="nomargin-top"><span class="codelink"><a href="Priithon.readerHIS-pysrc.html">source&nbsp;code</a></span></p>
<p>Priithon: Hamamatsu Image Sequence file format reader</p>

<hr />
<div class="fields">      <p><strong>Author:</strong>
        Sebastian Haase &lt;seb.haase+Priithon@gmail.com&gt;
      </p>
      <p><strong>License:</strong>
        BSD license - see LICENSE file
      </p>
</div><!-- ==================== CLASSES ==================== -->
<a name="section-Classes"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Classes</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-Classes"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="Priithon.readerHIS.ndarray_inHisFile-class.html" class="summary-name">ndarray_inHisFile</a>
    </td>
  </tr>
</table>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Functions</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-Functions"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
<tr class="private">
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="_try_openHIS_fastMap"></a><span class="summary-sig-name">_try_openHIS_fastMap</span>(<span class="summary-sig-arg">m</span>)</span></td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Priithon.readerHIS-pysrc.html#_try_openHIS_fastMap">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="Priithon.readerHIS-module.html#openHIS" class="summary-sig-name">openHIS</a>(<span class="summary-sig-arg">fn</span>,
        <span class="summary-sig-arg">mode</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">r</code><code class="variable-quote">'</code></span>)</span><br />
      open Hamamatsu Image Sequence...</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Priithon.readerHIS-pysrc.html#openHIS">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="readSection"></a><span class="summary-sig-name">readSection</span>(<span class="summary-sig-arg">m</span>,
        <span class="summary-sig-arg">offsetSect</span>=<span class="summary-sig-default">0</span>)</span><br />
      m:          numpy memmap of a file offsetSect: offset of first byte 
      of section to be read</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Priithon.readerHIS-pysrc.html#readSection">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="loadHISsec"></a><span class="summary-sig-name">loadHISsec</span>(<span class="summary-sig-arg">fn</span>,
        <span class="summary-sig-arg">sec</span>=<span class="summary-sig-default">0</span>)</span></td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Priithon.readerHIS-pysrc.html#loadHISsec">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="loadHISsects"></a><span class="summary-sig-name">loadHISsects</span>(<span class="summary-sig-arg">fn</span>,
        <span class="summary-sig-arg">secStart</span>=<span class="summary-sig-default">0</span>,
        <span class="summary-sig-arg">secEnd</span>=<span class="summary-sig-default">1</span>,
        <span class="summary-sig-arg">stride</span>=<span class="summary-sig-default">1</span>)</span></td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Priithon.readerHIS-pysrc.html#loadHISsects">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
</table>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Variables</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-Variables"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="mmap_shape"></a><span class="summary-name">mmap_shape</span> = <code title="None">None</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="Priithon.readerHIS-module.html#dtypeHIS" class="summary-name">dtypeHIS</a> = <code title="dtype([('magic', '|S2'), ('ComLen', '&lt;u2'), ('iDX', '&lt;u2'), ('iDY', '&lt;\
u2'), ('iX', '&lt;u2'), ('iY', '&lt;u2'), ('pixType', '&lt;u2'), ('numImgs', '&lt;\
u4'), ('numChan', '&lt;u2'), ('chan', '&lt;u2'), ('timeStamp', '&lt;f8'), ('mar\
ker', '&lt;u4'), ('miscinfo', '|i1', 30)])">dtype([('magic', '|S2'), ('ComLen', '&lt;u2'), ('iDX',<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="Priithon.readerHIS-module.html#hisType2numpyDtype" class="summary-name">hisType2numpyDtype</a> = <code title="{1: &lt;type 'numpy.uint8'&gt;,
 2: &lt;type 'numpy.uint16'&gt;,
 3: &lt;type 'numpy.uint32'&gt;,
 11: ('RGB',
      (&lt;type 'numpy.uint8'&gt;,
       &lt;type 'numpy.uint8'&gt;,
       &lt;type 'numpy.uint8'&gt;)),
 12: ('RGB', (&lt;type 'numpy.uint16'&gt;, &lt;type 'numpy.uint16'&gt;, &lt;type 'num\
..."><code class="variable-group">{</code>1<code class="variable-op">: </code>&lt;type 'numpy.uint8'&gt;<code class="variable-op">, </code>2<code class="variable-op">: </code>&lt;type 'numpy<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></a>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Function Details</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-FunctionDetails"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
</table>
<a name="openHIS"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">openHIS</span>(<span class="sig-arg">fn</span>,
        <span class="sig-arg">mode</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">r</code><code class="variable-quote">'</code></span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="Priithon.readerHIS-pysrc.html#openHIS">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

open Hamamatsu Image Sequence
return 3d array of all sections
if only the first section has a non-zero length variable comment entry
   (or no sections have a comment) 
   &quot;fast mapping&quot; should work and the whole file can be memmap'ed into one
   3D memmap array, with a special `HIS` attribute containing
      hdr0 = hisHdr0      # HIS-header info of first section
      comment0 = comment  # comment of first section
      hdr = a['hdr']      # HIS-header info all sections
           # NOTE:  `hdr[0]` IS 'CORRUPT' !!! DON'T USE THIS 1
                    USE `hdr0` INSTEAD !!!! 
otherwise
   this returns a mockNDarray of memmaped sections
   each section contains a HIS attribute,
      which contains hdr, offsetNext and comment

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<br />
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Variables Details</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-VariablesDetails"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
</table>
<a name="dtypeHIS"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">dtypeHIS</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
dtype([('magic', '|S2'), ('ComLen', '&lt;u2'), ('iDX', '&lt;u2'), ('iDY', '&lt;<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
u2'), ('iX', '&lt;u2'), ('iY', '&lt;u2'), ('pixType', '&lt;u2'), ('numImgs', '&lt;<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
u4'), ('numChan', '&lt;u2'), ('chan', '&lt;u2'), ('timeStamp', '&lt;f8'), ('mar<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ker', '&lt;u4'), ('miscinfo', '|i1', 30)])
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<a name="hisType2numpyDtype"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">hisType2numpyDtype</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code>1<code class="variable-op">: </code>&lt;type 'numpy.uint8'&gt;<code class="variable-op">,</code>
 2<code class="variable-op">: </code>&lt;type 'numpy.uint16'&gt;<code class="variable-op">,</code>
 3<code class="variable-op">: </code>&lt;type 'numpy.uint32'&gt;<code class="variable-op">,</code>
 11<code class="variable-op">: </code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">RGB</code><code class="variable-quote">'</code><code class="variable-op">,</code>
      <code class="variable-group">(</code>&lt;type 'numpy.uint8'&gt;<code class="variable-op">,</code>
       &lt;type 'numpy.uint8'&gt;<code class="variable-op">,</code>
       &lt;type 'numpy.uint8'&gt;<code class="variable-group">)</code><code class="variable-group">)</code><code class="variable-op">,</code>
 12<code class="variable-op">: </code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">RGB</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-group">(</code>&lt;type 'numpy.uint16'&gt;<code class="variable-op">, </code>&lt;type 'numpy.uint16'&gt;<code class="variable-op">, </code>&lt;type 'num<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="Priithon-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://code.google.com/p/priithon">Priithon</a></th>
          </tr></table></th>
  </tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
  <tr>
    <td align="left" class="footer">
    Generated by Epydoc 3.0.1 on Mon Nov 22 14:59:33 2010
    </td>
    <td align="right" class="footer">
      <a target="mainFrame" href="http://epydoc.sourceforge.net"
        >http://epydoc.sourceforge.net</a>
    </td>
  </tr>
</table>

<script type="text/javascript">
  <!--
  // Private objects are initially displayed (because if
  // javascript is turned off then we want them to be
  // visible); but by default, we want to hide them.  So hide
  // them unless we have a cookie that says to show them.
  checkCookie();
  // -->
</script>
</body>
</html>
